• Journal of Microbiology
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• v.44 no.4
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• pp.369-374
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• 2006

To investigate the mechanism of salt tolerance of gram-positive moderately halophilic bacteria, two-dimensional gel electrophoresis (2-D PAGE) was employed to achieve high resolution maps of proteins of Halobacillus dabanensis $D-8^T$. Approximately 700 spots of proteins were identified from these 2-D PAGE maps. The majority of these proteins had molecular weights between 17.5 and 66 kDa, and most of them were distributed between the isoelectric points (pI) 4.0 and 5.9. Some protein spots were distributed in the more acidic region of the 2-D gel (pI <4.0). This pattern indicated that a number of proteins in the strain $D-8^T$ are acidic. To understand the adaptation mechanisms of moderately halophilic bacteria in response to sudden environmental changes, differential protein profiles of this strain were investigated by 2-D PAGE and $Imagemaster^{TM}$ 2D Platinum software after the cells were subjected to salt shock of 1 to 25% salinity for 5 and 50 min. Analysis showed 59 proteins with an altered level of expression as the result of the exposure to salt shock. Eighteen proteins had increased expression, S proteins were induced, and the expression of 33 proteins was down-regulated. Eight of the up-regulated proteins were identified using MALDI-TOF/MS and MASCOT, and were similar to proteins involved in signal transduction, proteins participating in energy metabolism pathways and proteins involved in stress.

• Proceedings of the PSK Conference
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• 2003.10b
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• pp.147.2-147.2
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• 2003

A fast and matrix-assisted laser desorption/ionization-mass spectrometry compatible protein staining method in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis is described. It is based on the counterion dye staining method that employs oppositely charged two dyes, Zincon and Ethyl Violet to form an ion-pair complex. It is safe to use since the methanol used previously in staining solution was replaced with ethanol, which is not toxic. The protocol including fixing, staining and quick washing steps can be completed in 1 to 1.5 h depending upon gel thickness. (omitted)

• Journal of Plant Biotechnology
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• v.37 no.2
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• pp.196-204
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• 2010

With the completion of genome sequencing of several organisms, attention has been focused to determine the function and functional network of proteins by proteome analysis. The recent techniques of proteomics have been advanced quickly so that the high-throughput and systematic analyses of cellular proteins are enabled in combination with bioinformatics tools. Furthermore, the development of proteomic techniques helps to elucidate the functions of proteins under stress or diseased condition, resulting in the discovery of biomarkers responsible for the biological stimuli. Ultimate goal of proteomics orients toward the entire proteome of life, subcellular localization, biochemical activities, and their regulation. Comprehensive analysis strategies of proteomics can be classified as three categories: (i) protein separation by 2-dimensional gel electrophoresis (2-DE) or liquid chromatography (LC), (ii) protein identification by either Edman sequencing or mass spectrometry (MS), and (iii) quanitation of proteome. Currently MS-based proteomics turns shiftly from qualitative proteome analysis by 2-DE or 2D-LC coupled with off-line matrix assisted laser desorption ionization (MALDI) and on-line electrospray ionization (ESI) MS, respectively, to quantitative proteome analysis. Some new techniques which include top-down mass spectrometry and tandem affinity purification have emerged. The in vitro quantitative proteomic techniques include differential gel electrophoresis with fluorescence dyes, protein-labeling tagging with isotope-coded affinity tag, and peptide-labeling tagging with isobaric tags for relative and absolute quantitation. In addition, stable isotope labeled amino acid can be in vivo labeled into live culture cells through metabolic incorporation. MS-based proteomics extends to detect the phosphopeptide mapping of biologically crucial protein known as one of post-translational modification. These complementary proteomic techniques contribute to not only the understanding of basic biological function but also the application to the applied sciences for industry.

• Journal of Microbiology and Biotechnology
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• v.21 no.2
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• pp.136-146
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• 2011

This study provides first-hand proteomic data on the survival strategy of Anabaena sp. PCC 7120 when subjected to long-term iron-starvation conditions. 2D-gel electrophoresis followed by MALDI-TOF/MS analysis of iron-deficient Anabaena revealed significant and reproducible alterations in ten proteins, of which six are associated with photosynthesis and respiration, three with the antioxidative defense system, and the last, hypothetical protein all1861, conceivably connected with iron homeostasis. Iron-starved Anabaena registered a reduction in growth, photosynthetic pigments, PSI, PSII, whole-chain electron transport, carbon and nitrogen fixation, and ATP and NADPH content. The kinetics of hypothetical protein all1861 expression, with no change in expression until day 3, maximum expression on the $7^{th}$ day, and a decline in expression from the $15^{th}$ day onward, coupled with in silico analysis, suggested its role in iron sequestration and homeostasis. Interestingly, the up-regulated FBP-aldolase, Mn/Fe-SOD, and all1861 all appear to assist the survival of Anabeana subjected to iron-starvation conditions. Furthermore, the $N_2$-fixation capabilities of the iron-starved Anabaena encourage us to recommend its application as a biofertilizer, particularly in iron-limited paddy soils.

• 한국생물공학회:학술대회논문집
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• 2005.10a
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• pp.674-679
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• 2005

With addition of uracil during fermentation, the production rate of $1,3-{\beta}-glucan(curdlan)$ was enhanced. Since uracil was used as precursor of UDP-Glucose, the UDP-glucose level was increased and further glucan synthesis rate was increased.

• Journal of Plant Biotechnology
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• v.39 no.1
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• pp.81-92
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• 2012

Two-dimensional gel electrophoresis (2-DGE) is one of the most important technologies for high-resolution separation of proteins for proteomics. In this study, we present a detail 2-DGE protocol which allows detection and quantification of total plant proteins separated on gels to improve matching in image analysis. This protocol highlighted here may be useful for researchers, who like to first study for the development of protein biomarkers involved in development, biotic and abiotic stresses in plant.

• Food Science and Biotechnology
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• v.18 no.1
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• pp.249-252
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• 2009

Two-dimensional gel electrophoresis (2-DE) was employed to assess the thermo-tolerance characteristics of Bifrdobacterium infantis ATCC 27920 to mild heat adaptation. When exposed to various heat levels, pH, and hydrogen peroxide ($H_2O_2$) stress conditions, B. infantis ATCC 27920 exhibited high level of stress resistance. Under mild-heat treatment ($46^{\circ}C$), no significant change in viability level was observed after 2 hr. Interestingly, improved viability was observed in mild-heat adapted ($46^{\circ}C$ for 1 hr) cultures exposed to $55^{\circ}C$, in comparison to control experiments. Viability was not affected by pH, bile, and $H_2O_2$ stress conditions. 2-DE analysis revealed those mild-heat adaptation up-regulated 4 proteins and down-regulated 3 proteins. Among these protein spots, isopropyhnalate dehydratase (leuD), glycosyltransferase (glgA), and ribosomal protein L5 (rp1E) were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALD1-TOF/MS).

• BMB Reports
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• v.38 no.3
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• pp.307-313
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• 2005

Thiobacillus ferrooxidans is one of the most important bacterium used in bioleaching, and can utilize $Fe^{2+}$ or sulphide as energy source. Growth curves for Thiobacillus ferrooxidans have been tested, which show lag, logarithmic, stationary and aging phases as seen in other bacteria. The logarithmic phases were from 10 to 32 hours for Thiobacillus ferrooxidans cultivated with $Fe^{2+}$ and from 4 to 12 days for Thiobacillus ferrooxidans cultivated with elemental sulphur. Differences of protein patterns of Thiobacillus ferrooxidans growing on elemental sulphur and $Fe^{2+}$ separately were investigated after cultivation at $30^{\circ}C$ by the analysis of two-dimensional gel electrophoresis (2-DE), matrix-assisted laser desorption/ ionization (MALDI)-Mass spectrometry and ESI-MS/MS. From the 7 identified protein spots, 11 spots were found more abundant when growing on elemental sulphur. By contrast 6 protein spots were found decreased at elemental cultivation condition. Among the proteins identified, cytochrome C have been previously identified as necessary elements of electron-transfering pathway for Thiobacillus ferrooxidans to oxidize $Fe^{2+}$; ATP synthase alpha chain and beta are expressed increased when Thiobacillus ferrooxidans cultivated with $Fe^{2+}$ as energy source. ATP synthase Beta chain is the catalytic subunit, and ATP synthase alpha chain is a regulatory subunit. The function of ATPase produces ATP from ADP in the presence of a proton gradient across the membrane.

• Journal of the Korea Society for Simulation
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• v.20 no.2
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• pp.77-85
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• 2011

It is believed that the anomalies or diseases of human organs are identified by the analysis of the patterns. This paper proposes a new classification technique for the identification of cancer disease using the proteome patterns obtained from two-dimensional polyacrylamide gel electrophoresis(2-D PAGE). In the new classification method, three different classification methods such as support vector machine(SVM), multi-layer perceptron(MLP) and k-nearest neighbor(k-NN) are extended by multi-boosting method in an array of subclassifiers and the results of each subclassifier are merged by ensemble method. Genetic algorithm was applied to obtain optimal feature set in each subclassifier. We applied our method to empirical data set from cancer research and the method showed the better accuracy and more stable performance than single classifier.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.1
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• pp.367-372
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• 2013

Effects of the Epstein-Barr virus (EBV) on cellular protein expression are essential for viral pathogenesis. To characterize the cellular response to EBV infection, differential proteomes of gastric epithelial AGS cells were analyzed with two-dimensional gel electrophoresis (2-DE) followed by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) and liquid chromatography electrospray/ionization ion trap (LC-ESI-IT) mass spectrometry identification. Mass spectrometry identified 9 altered cellular proteins, including 5 up-regulated and 4 down-regulated proteins after EBV infection. Notably 2-DE analysis revealed that EBV infection induced increased expression of heat shock cognate 71 kDa protein, actin cytoplasmic 1, pyridoxine-5'-phosphate oxidase, caspase 9, and t-complex protein 1 subunit alpha. In addition, EBV infection considerably suppressed those cellular proteins of zinc finger protein 2, cyclin-dependent kinase 2, macrophage-capping protein, and growth/differentiation factor 11. Furthermore, the differential expressional levels of partial proteins (cyclin-dependent kinase 2 and caspase 9) were confirmed by Western blot analysis.Thus, this work effectively provided useful protein-related information to facilitate further investigation of the mechanisms underlying EBV infection and pathogenesis.